基于m6A去甲基化酶ALKBH5的胃癌预后及免疫微环境特征的鉴定与验证

Identification and validation of signature for prognosis and immune microenvironment in gastric cancer based on m6A demethylase ALKBH5.

作者信息

Ji Tiannan, Gao Xiaohui, Li Dan, Huai Siyuan, Chi Yajing, An Xian, Ji Wenyu, Yang Siming, Li Jianxiong

机构信息

Medical School of Chinese PLA, Beijing, China.

Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China.

出版信息

Front Oncol. 2023 Jan 6;12:1079402. doi: 10.3389/fonc.2022.1079402. eCollection 2022.

DOI:10.3389/fonc.2022.1079402

PMID:36686788

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9853004/

Abstract

BACKGROUND

N6-methyladenosine (m6A) RNA regulators play important roles in cancers, but their functions and mechanism have not been demonstrated clearly in gastric cancer (GC).

METHODS

In this study, the GC samples with clinical information and RNA transcriptome were downloaded from The Cancer Genome Atlas database. The different expression genes were compared by the absolute value and median ± standard deviation. Samples with complete information were randomly divided into a training dataset and a test dataset. The differential expression genes (DEGs) between -low and -high subgroups were identified in the training dataset and constructed a risk model by Cox and least absolute shrinkage and selection operator regression. The model was testified in test datasets, overall survival (OS) was compared with the Kaplan-Meier method, and immune cell infiltration was calculated by the CIBERSORT algorithm in the low-risk and high-risk subgroups based on the model. The protein levels of ALKBH5 were detected with immunohistochemistry. The relative expression of messenger-ribonucleic acid (mRNA) was detected with quantitative polymerase chain reaction.

RESULTS

was the only regulator whose expression was lower in tumor samples than that in normal samples. The low expression of led to the poor OS of GC patients and seemed to be an independent protective factor. The model based on -regulated genes was validated in both datasets (training/test) and displayed a potential capacity to predict a clinical prognosis. Gene Ontology analysis implied that the DEGs were involved in the immune response; CIBERSORT results indicated that ALKBH5 and its related genes could alter the immune microenvironment of GC. The protein levels of ALKBH5 were verified as lowly expressed in GC tissues. and were downregulated with knockdown.

CONCLUSIONS

In this study, we found that ALKBH5 might be a suppressor of GC; ALKBH5 and its related genes were latent biomarkers and immunotherapy targets.

摘要

背景

N6-甲基腺苷（m6A）RNA调节因子在癌症中发挥重要作用，但其在胃癌（GC）中的功能和机制尚未明确。

方法

本研究从癌症基因组图谱数据库下载了具有临床信息和RNA转录组的GC样本。通过绝对值和中位数±标准差比较差异表达基因。将具有完整信息的样本随机分为训练数据集和测试数据集。在训练数据集中鉴定-low和-high亚组之间的差异表达基因（DEG），并通过Cox和最小绝对收缩和选择算子回归构建风险模型。在测试数据集中验证该模型，采用Kaplan-Meier方法比较总生存期（OS），并基于该模型通过CIBERSORT算法计算低风险和高风险亚组中的免疫细胞浸润。用免疫组织化学检测ALKBH5的蛋白水平。用定量聚合酶链反应检测信使核糖核酸（mRNA）的相对表达。

结果

是唯一在肿瘤样本中表达低于正常样本的调节因子。的低表达导致GC患者的OS较差，似乎是一个独立的保护因素。基于调节基因的模型在两个数据集（训练/测试）中均得到验证，并显示出预测临床预后的潜在能力。基因本体分析表明DEG参与免疫反应；CIBERSORT结果表明ALKBH5及其相关基因可改变GC的免疫微环境。在GC组织中验证ALKBH5的蛋白水平低表达。敲低后和下调。